Clean breeding doesnt affect the game at all its just a extra challenge to the game. Clean breeding is just making sure that there are no instances of Inbreeding in the family tree. for example

Clean Lioness:
https://www.lioden.com/lion.php?id=794163676409 (clean G9 No instances of Inbreeding)
Dirty Lioness:
https://www.lioden.com/lion.php?id=794172352440 (Dirty Lion 1 Instance of Inbreeding)

Let me know if this helps or if i should explain a little more.

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When you look into a lion's heritage and there is no inbreeding throughout the entire lineage, the lion is clean. To breed cleanly, you have to make sure the same lion isn't in the heritage more than once.

If a G2 stud has, for example, Beauregard as their father, and you want to breed them with one of your lionesses, you have to make sure she doesn't have Beauregard in her heritage at all.

The exception would be if she has his name somewhat far back in her heritage, because it could be an unrelated iteration of Beauregard. Click on his name in both of their heritage to see if it brings you to the living Beauregard's page or if it takes you to the dynasty. If one takes you to the living king and one takes you to the dynasty, they are both different heritage and will not inbreed the cubs.

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I have a guide up on specifically Low Gen breeding, which is the style of Clean Breeding most commonly used if you're curious! https://www.lioden.com/topic.php?id=304429467319

Basically, if you'd like to clean breed I'd recommend sticking to NCLs or maybe G2 lions for your breeding projects; be sure that your king is also clean, though! 'No inbreeding on the first page' is still dirty if a lion is inbred further down their line, and like Terrinthia pointed out, even if the inbreeding marker doesn't show up visually on a page a lion can still be inbred if the same lion is in their heritage twice.

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